/// <summary>
/// Generate the mass error scatter plots and mass error histogram plots, saving as PNG files
/// </summary>
/// <param name="psmResults"></param>
/// <param name="fixedMzMLFileExists"></param>
/// <param name="haveScanTimes"></param>
public override bool GeneratePNGPlots(IReadOnlyCollection <IdentData> psmResults, bool fixedMzMLFileExists, bool haveScanTimes)
{
if (!ValidateOutputDirectories(BaseOutputFilePath))
{
return(false);
}
var metadataFileInfo = new MetadataFileInfo(BaseOutputFilePath, Options);
var scatterPlotSuccess = ErrorScatterPlotsToPng(psmResults, metadataFileInfo.MassErrorPlotFile.FullName, fixedMzMLFileExists, haveScanTimes);
if (scatterPlotSuccess)
{
Console.WriteLine("Generated {0}", metadataFileInfo.MassErrorPlotFile.FullName);
}
else
{
Console.WriteLine("Error generating {0}", metadataFileInfo.MassErrorPlotFile.FullName);
}
var histogramPlotSuccess = ErrorHistogramsToPng(psmResults, metadataFileInfo.HistogramPlotFile.FullName, fixedMzMLFileExists);
if (histogramPlotSuccess)
{
Console.WriteLine("Generated {0}", metadataFileInfo.HistogramPlotFile.FullName);
}
else
{
Console.WriteLine("Error generating {0}", metadataFileInfo.HistogramPlotFile.FullName);
}
return(scatterPlotSuccess && histogramPlotSuccess);
}
/// <summary>
/// Generate the mass error scatter plots and mass error histogram plots, saving as PNG files
/// </summary>
/// <param name="scanData"></param>
/// <param name="fixedMzMLFileExists"></param>
/// <param name="haveScanTimes"></param>
public override bool GeneratePNGPlots(IReadOnlyCollection <IdentData> scanData, bool fixedMzMLFileExists, bool haveScanTimes)
{
var metadataFileInfo = new MetadataFileInfo(BaseOutputFilePath, Options);
if (!ValidateOutputDirectories(BaseOutputFilePath))
{
return(false);
}
var histogramPlotDataExported = ExportHistogramPlotData(
scanData, metadataFileInfo.BaseOutputFile, fixedMzMLFileExists,
out var errorHistogramsExportFileName);
if (!histogramPlotDataExported)
{
return(false);
}
var scatterPlotDataExported = ExportScatterPlotData(
scanData, fixedMzMLFileExists, haveScanTimes, metadataFileInfo.BaseOutputFile,
out var massErrorVsTimeExportFileName,
out var massErrorVsMassExportFileName);
if (!scatterPlotDataExported)
{
return(false);
}
metadataFileInfo.ErrorHistogramsExportFileName = errorHistogramsExportFileName;
metadataFileInfo.MassErrorVsTimeExportFileName = massErrorVsTimeExportFileName;
metadataFileInfo.MassErrorVsMassExportFileName = massErrorVsMassExportFileName;
var success = GeneratePlotsWithPython(metadataFileInfo);
return(success);
}
/// <summary>
/// Call the Python script to create the plots
/// </summary>
/// <returns>True if success, otherwise false</returns>
/// <remarks>Call ErrorHistogramsToPng and ErrorScatterPlotsToPng prior to calling this method</remarks>
private bool GeneratePlotsWithPython(MetadataFileInfo metadataFileInfo)
{
if (!PythonInstalled)
{
NotifyPythonNotFound("Could not find the python executable");
return(false);
}
if (metadataFileInfo.BaseOutputFile.Directory == null)
{
OnErrorEvent("Unable to determine the parent directory of the base output file: " + metadataFileInfo.BaseOutputFile.FullName);
return(false);
}
if (!metadataFileInfo.BaseOutputFile.Directory.Exists)
{
metadataFileInfo.BaseOutputFile.Directory.Create();
}
var workDir = metadataFileInfo.BaseOutputFile.Directory.FullName;
var exeDirectory = Path.GetDirectoryName(System.Reflection.Assembly.GetExecutingAssembly().Location);
if (exeDirectory == null)
{
OnErrorEvent("Unable to determine the path to the directory with the PPMErrorCharter executable");
return(false);
}
var pythonScriptFile = new FileInfo(Path.Combine(exeDirectory, "PPMErrorCharter_Plotter.py"));
if (!pythonScriptFile.Exists)
{
OnErrorEvent("Python plotting script not found: " + pythonScriptFile.FullName);
return(false);
}
var baseOutputName = metadataFileInfo.BaseOutputFile.Name;
var metadataFile = new FileInfo(Path.Combine(workDir, "MZRefinery_Plotting_Metadata.txt"));
OnDebugEvent("Creating " + metadataFile.FullName);
using (var writer = new StreamWriter(new FileStream(metadataFile.FullName, FileMode.Create, FileAccess.Write, FileShare.ReadWrite)))
{
var plotFilesDefined = 0;
if (metadataFileInfo.HistogramPlotFile != null)
{
writer.WriteLine("HistogramPlotFilePath=" + metadataFileInfo.HistogramPlotFile.FullName);
plotFilesDefined++;
}
if (metadataFileInfo.MassErrorPlotFile != null)
{
writer.WriteLine("MassErrorPlotFilePath=" + metadataFileInfo.MassErrorPlotFile.FullName);
plotFilesDefined++;
}
if (plotFilesDefined < 2)
{
writer.WriteLine("BaseOutputName=" + baseOutputName);
metadataFileInfo.HistogramPlotFile = new FileInfo(Path.Combine(metadataFileInfo.BaseOutputFile.FullName, baseOutputName + "_Histograms.png"));
metadataFileInfo.MassErrorPlotFile = new FileInfo(Path.Combine(metadataFileInfo.BaseOutputFile.FullName, baseOutputName + "_MassErrors.png"));
}
writer.WriteLine("HistogramData=" + metadataFileInfo.ErrorHistogramsExportFileName);
writer.WriteLine("MassErrorVsTimeData=" + metadataFileInfo.MassErrorVsTimeExportFileName);
writer.WriteLine("MassErrorVsMassData=" + metadataFileInfo.MassErrorVsMassExportFileName);
}
var args = PathUtils.PossiblyQuotePath(pythonScriptFile.FullName) + " " + PathUtils.PossiblyQuotePath(metadataFile.FullName);
OnDebugEvent("{0} {1}", PythonPath, args);
var progRunner = new ProgRunner
{
Arguments = args,
CreateNoWindow = true,
MonitoringInterval = 2000,
Name = "PythonPlotter",
Program = PythonPath,
Repeat = false,
RepeatHoldOffTime = 0,
WorkDir = workDir
};
RegisterEvents(progRunner);
const int MAX_RUNTIME_SECONDS = 600;
const int MONITOR_INTERVAL_MILLISECONDS = 1000;
var runtimeExceeded = false;
try
{
// Start the program executing
progRunner.StartAndMonitorProgram();
var startTime = DateTime.UtcNow;
// Loop until program is complete, or until MAX_RUNTIME_SECONDS seconds elapses
while (progRunner.State != ProgRunner.States.NotMonitoring)
{
ProgRunner.SleepMilliseconds(MONITOR_INTERVAL_MILLISECONDS);
if (DateTime.UtcNow.Subtract(startTime).TotalSeconds < MAX_RUNTIME_SECONDS)
{
continue;
}
OnErrorEvent("Plot creation with Python has taken more than {0:F0} minutes; aborting", MAX_RUNTIME_SECONDS / 60.0);
progRunner.StopMonitoringProgram(kill: true);
runtimeExceeded = true;
break;
}
}
catch (Exception ex)
{
OnErrorEvent("Exception creating plots using Python", ex);
return(false);
}
if (runtimeExceeded)
{
return(false);
}
// Examine the exit code
if (progRunner.ExitCode == 0)
{
OnStatusEvent("Generated plots; see:\n " + metadataFileInfo.HistogramPlotFile?.FullName + "\nand\n " + metadataFileInfo.MassErrorPlotFile?.FullName);
if (DeleteTempFiles)
{
// Delete the temp export files
try
{
metadataFile.Delete();
File.Delete(Path.Combine(workDir, metadataFileInfo.ErrorHistogramsExportFileName));
File.Delete(Path.Combine(workDir, metadataFileInfo.MassErrorVsTimeExportFileName));
File.Delete(Path.Combine(workDir, metadataFileInfo.MassErrorVsMassExportFileName));
}
catch (Exception ex)
{
OnErrorEvent("Error deleting files: " + ex.Message);
}
}
else
{
ConsoleMsgUtils.ShowDebug("{0}\n {1}\n {2}\n {3}\n {4}",
"Not deleting the following temporary files since debug mode is enabled",
metadataFile.FullName,
Path.Combine(workDir, metadataFileInfo.ErrorHistogramsExportFileName),
Path.Combine(workDir, metadataFileInfo.MassErrorVsTimeExportFileName),
Path.Combine(workDir, metadataFileInfo.MassErrorVsMassExportFileName));
}
return(true);
}
OnErrorEvent("Python ExitCode = " + progRunner.ExitCode);
return(false);
}